According to the Department of Fisheries and Wildlife Sciences, Virginia Tech., detoxification of ammonia occurs in biofilters through the process of nitrification.
Nitrification refers to the bacterial conversion of ammonia nitrogen (NH4/NH3) to the less toxic NO2 and finally to “non-toxic” NO3.
The bacterial nitrification process requires a suitable surface on the biofilter upon which the bacteria grow (biofilter media) pumping a continuous flow of tank-water through the biofilter and maintaining normal water temperature and good water quality.
Two groups of aerobic (oxygen requiring) nitrifying bacteria are needed. Nitrosomonas bacteria convert NH4/NH3 to NO2 (they oxidize toxic ammonia excreted by fish-gills/urine and excreta into less toxic nitrite). The nitrobacter bacteria convert NO2 to NO3 (they oxidize nitrite to largely non-toxic nitrate).
Bacterial nitrification is an aerobic process which requires oxygen. For every 1 mg of ammonia converted 5 mg of dissolved oxygen is consumed and an additional 5 mg of dissolved oxygen is required to satisfy the oxygen demand of the bacteria involved with the conversion. Therefore, tanks with large numbers of fish and heavy ammonia loads will require plenty of oxygen before and after the biofilter process.
Bacterial nitrification is an acidifying process, but is most efficient when the water pH is maintained between 7 and 8 and the water temperature is about 27-28 C. Acid water, (less than pH 6.5) inhibits bacterial nitrification and should be avoided. Soft, acidic waters may require addition of carbonates (calcium carbonate, sodium bicarbonate) to buffer the water.
Biofilters consist of actively growing bacteria attached to surfaces. Biofilters can fail if the bacteria die or are inhibited by natural aging, toxicity from chemicals, (for example, fish disease treatment), lack of oxygen, low pH. Biofilters, are designed so that aging cells can be sloughed off to create space for active new bacterial growth. However, there are situations, (e.g., cleaning too vigorously) where all bacteria are removed, or if chemical addition to tank water to fight fish disease results in biofilter failure then the water in the system should be exchanged. The biofilter would then have to be reactivated (taking 3 to 4 weeks) and the water pH adjusted to optimum levels.
Activating a new biofilter, (i.e., developing a healthy population of nitrifying bacteria capable of removing ammonia and nitrite produced at normal feeding rates) requires one to three months. Many fish die during this period of biofilter activation.